Diagnostic value of metagenomic next-generation sequencing of lower respiratory tract specimen for the diagnosis of suspected Pneumocystis jirovecii pneumonia

Figures & data

Table 1. Comparison of diagnostic performance among mNGS, PCR, GMS staining and serum BG.

Methods	mNGS		PCR		GMS		Serum BG
	+	−	+	−	+	−	+	−
PCP	48	4	42	5	4	39	35	13
non-PCP	13	90	4	36	0	86	11	75
Sensitivity	92.3%		89.4%		9.3%		72.9%
(95% CI, p-value)	(81.5–97.9)		(76.9–96.4, .739)		(2.6–22.1, <.001)		(58.2–84.7, .003)
Specificity	87.4%		90.0%		100.0%		87.2%
(95% CI, p-value)	(79.4–93.1)		(76.3–97.2, .739)		(95.8–100, <.001)		(78.3–93.4, .835)
PPV	78.7%		91.3%		100.0%		76.1%
(95% CI, p-value)	(66.3–88.1)		(79.2–97.6, .767)		(39.8–100, .250)		(61.2–87.4, .738)
NPV	95.7%		87.8%		68.8%		85.2%
(95% CI, p-value)	(89.5–98.8)		(73.8–95.9, .773)		(59.9–76.8, <.001)		(76.1–91.9, .003)

mNGS: metagenomic next-generation sequencing; PCR: polymerase chain reaction; GMS: Gomori methenamine silver; BG: 1,3-β-d-Glucan; PCP: Pneumocystis jirovecii pneumonia; CI: confidence interval; PPV: positive predict value; NPV: negative predict value. Serum BDG ≥ 100 pg/ml was considered positive. P-values were determined in comparison with mNGS.

Figure 1. Sequencing reads among PCP and non-PCP patients with P. jirovecii detected by mNGS. PCP group: n = 48, median 168; non-PCP group: n = 13, median 3. Error bar, median with IQR.

Figure 2. ROC curves for BG, mNGS, BG + mNGS and PCR in diagnosing PCP. (A) serum BG. (B) mNGS. (C) Combination of mNGS and serum BG. (D) PCR.

Figure 3. Distribution of pathogens detected by mNGS of lower respiratory tract specimens from PCP and non-PCP patients. (A) Top 10 co-pathogens identified from PCP patients. (B) Top 10 co-pathogens identified from patients with non-PCP pneumonia. (C) Composition of detected pathogens based on microbial types. P. jirovecii was not taken into calculation when cases were attributed to certain categories. CMV: cytomegalovirus; EBV: Epstein-Barr virus; HSV: herpes simplex virus; HHV: human herpes virus.

Figure 4. Distribution of oxygenation Indexes (PaO₂/FiO₂) among patients with PCP.

Table 2. Clinical characteristics of PCP and non-PCP patients.

Variables	PCP patients (n = 52)	Non-PCP patients (n = 103)
Sex (male)	29 (55.8%)	52 (50.5%)
Age (years)	59 (48–70)	55 (40–75)
Immunocompromised conditions
Rheumatic autoimmune diseases	25 (48.1%)	34 (33.0%)
Solid tumors	10 (19.2%)	23 (22.3%)
Hematological malignancies	3 (5.8%)	10 (9.7%)
Organ transplantation	3 (5.8%)	1 (1.0%)
Medication
Corticosteroid Use^b	42 (80.8%)	43 (41.7%)
Dose of corticosteroids (mg)^a	40 (30–60)	20 (5–60)
Duration of corticotherapy (months)	2.5 (1–4)	4 (1–12)
Use of immunosuppressive agents^b	35 (67.3%)	37 (35.9%)
TMP-SMX as PCP prophylaxis	2 (3.8%)	10 (9.7%)
Symptoms
Fever at admission	36 (69.2%)	81 (78.6%)
Cough	31 (59.6%)	46 (44.7%)
Dyspnea^b	43 (82.7%)	45 (43.7%)
Laboratory and radiological indicators
White blood cells (10^9/L)	9.70 (5.59–12.69)	11.28 (3.45–23.60)
Lymphocytes (10^9/L)^Table Footnoteb	0.52 (0.31–1.00)	1.11 (0.53–3.79)
Lactate dehydrogenase (U/L)	510 (363–687)	248 (161–379)
1,3-β-d-Glucan assay ≥100 pg/ml^b	35/48 (72.9%)	11/84 (13.1%)
Ground-glass opacity in CT^b	46 (88.5%)	24 (23.3%)

^aThe dosage of corticosteroids was expressed as the prednisone equivalent (1 mg of prednisone equals 0.8 mg of ­methylprednisolone which equals 1 mg of prednisolone).

^bCharacteristics which were significantly different between PCP and non-PCP patients (p < 0.05).

Data were presented as number (percentage) or median (IQR).

Table 3. Managements and outcomes of PCP patients.

Variables	PCP patients (n = 52)
Treatments
TMP-SMX	51 (98.1%)
Clindamycin	20 (38.5%)
Clindamycin + primaquine	4 (7.7%)
Caspofungin	18 (34.6%)
High-flow nasal cannula	20 (38.5%)
Non-invasive ventilator	2 (3.8%)
Invasive ventilator	32 (61.5%)
ECMO	9 (17.3%)
Outcomes
ICU admission	43 (82.7%)
Length of ICU stay (days)	11 (3–26)
Length of hospital stay (days)	25.5 (12–39)
In-hospital mortality	12 (23.1%)
30-d mortality	19 (36.5%)

TMP-SMX: trimethoprim/sulfamethoxazole; ECMO: extracorporeal membrane oxygenation.

Data were presented as number (percentage) or median (IQR).

Data availability statement

The datasets generated and/or analyzed during the current study are available from the corresponding author upon reasonable request if permitted by Peking Union Medical College Hospital.